Clinical Genomics Report

Sample: TEST

Report Date: 2025-07-05 08:01

Pipeline: Rare Disease Variant Prioritization v1.0

Executive Summary

562

High Priority Variants

2565

Medium Priority Variants

1620

Low Priority Variants

4747

Total Variants

Clinical Interpretation

562 high-priority variants identified.
Multiple potential pathogenic variants suggest possible compound heterozygosity or phenotypic complexity.
Cancer predisposition genes identified. Recommend oncogenetics consultation.

Top 20 Prioritized Variants

CHROM POS REF ALT SYMBOL Consequence gnomAD_AF CADD_PHRED REVEL CLIN_SIG pathogenicity_score priority_score
0 22 16352119 A G TP53 missense_variant 0.0002 35.3835 0.9943 Pathogenic 10.0 15.0
1 22 16062289 G A CHEK2 missense_variant 0.0002 37.8899 0.7653 Pathogenic 10.0 15.0
2 22 16066471 GC G OTHER2 frameshift_variant 0.0006 32.4221 0.9718 Pathogenic 10.0 15.0
3 22 16229119 G A TP53 missense_variant 0.0002 33.1300 0.8067 Pathogenic 10.0 15.0
4 22 16181155 T A CHEK2 missense_variant 0.0002 32.7134 0.9859 Pathogenic 10.0 15.0
5 22 16335870 C T CDKN2A missense_variant 0.0002 30.4341 0.6549 Pathogenic 9.0 14.0
6 22 16163594 C G BRCA2 missense_variant 0.0002 24.9187 0.9438 Pathogenic 9.0 14.0
7 22 16341505 G A BRCA2 missense_variant 0.0002 23.7136 0.7969 Pathogenic 9.0 14.0
8 22 16362582 C A CHEK2 missense_variant 0.0002 25.1928 0.8090 Pathogenic 9.0 14.0
9 22 16142248 T G OTHER3 missense_variant 0.0004 34.8040 0.7951 Pathogenic 10.0 13.0
10 22 16150952 T A OTHER2 missense_variant 0.0008 38.9396 0.8794 Pathogenic 10.0 13.0
11 22 16071986 C T OTHER3 missense_variant 0.0004 32.2481 0.9903 Pathogenic 10.0 13.0
12 22 16117736 C T CDKN2A missense_variant 0.0004 33.5559 0.2751 Pathogenic 8.0 13.0
13 22 16315885 G A BRCA2 missense_variant 0.0010 33.7330 0.4105 Pathogenic 8.0 13.0
14 22 16060866 G A OTHER1 missense_variant 0.0006 34.3365 0.7663 Pathogenic 10.0 13.0
15 22 16355755 A G GENE2 missense_variant 0.0002 39.3427 0.9146 Pathogenic 10.0 13.0
16 22 16050627 G T GENE1 missense_variant 0.0004 34.6470 0.8614 Pathogenic 10.0 13.0
17 22 16232108 G A GENE1 missense_variant 0.0004 35.6921 0.8350 Pathogenic 10.0 13.0
18 22 16405095 C T OTHER3 missense_variant 0.0002 39.6613 0.8466 Pathogenic 10.0 13.0
19 22 16143946 A G OTHER3 missense_variant 0.9123 34.9471 0.9814 Pathogenic 10.0 12.0

Methodology

Prioritization Criteria
  • Population Frequency: gnomAD AF < 0.1%
  • Functional Impact: High/moderate consequence variants
  • Pathogenicity: CADD, REVEL, ClinVar scores
  • Gene Panels: Cancer predisposition genes
Scoring System
  • Frequency Score: 0-3 points (rarer = higher)
  • Consequence Score: 0-4 points
  • Pathogenicity Score: 0-10 points
  • Gene Panel Bonus: 0-2 points

This report is for research purposes. Clinical decisions should involve genetic counseling and additional testing.